It will then reach 0 and then go into minus figures. The only way to stop this is to kill the ESB container process. The inflight messages seem to be connections to the FTP which have not timedout or been released as every now and again i see exceptions such as:

You can't specify a shutdown timeout for each route; there is a global timeout used in the DefaultShutdownStrategy of 300 seconds. You could lower the global value or you could override the DefaultShutdownStrategy with your own. I would suggest trying to lower the timeouts as well (see http://camel.apache.org/ftp.html).